[ccp4bb] Postdoctoral position - Cryo-EM and Biochemistry of Molecular Motors

[Krishna Chinthalapudi]

Dear All,



We are excited to announce the opening of a joint postdoctoral scientist
position in the laboratories of Dr. Sarah Heissler and Dr. Krishna
Chinthalapudi at the Ohio State University. This exceptional opportunity
focuses on groundbreaking research to unravel the role of myosin motors and
cytoskeletal proteins in both health and disease. Our approach combines
cutting-edge structural biology techniques, including cryo-EM and X-ray
crystallography, with biochemical, biophysical, and cell biological methods
to investigate the structure and function of myosin motors, as well as
their regulation by cytoskeletal proteins.



Our laboratories are well equipped with state-of-the-art instrumentation
for the proposed studies and have generous access to a Titan Krios G3i
Cryo-TEM equipped with a BioQuantum imaging filter and a K3 direct electron
detector, imaging phase plates, and an image spherical aberration
corrector. In addition, our labs have access to a Glacios with a Falcon III
detector and a cryo-FIB at the world-class Center for Electron Microscopy
and Analysis (CEMAS) at the Ohio State University.



To be eligible for this position, candidates must hold a Ph.D. degree and
possess considerable experience in structural biology. If you also have a
background in molecular biology techniques, and/or high-resolution imaging,
it would be highly desirable. To apply for this exciting opportunity,
kindly email us your CV, a short cover letter detailing your research
experience and interests, and the contact information for three references
to Sarah Heissler (sarah.heiss...@osumc.edu) and Krishna Chinthalapudi (
krishna.chinthalap...@osumc.edu).



Best,

Krishna



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[ccp4bb] RCSB PDB file downloads DNS changes

[Jose Duarte]

RCSB PDB has recently introduced DNS names for programmatic access to PDB
archive downloads:

FTP: ftp://ftp.rcsb.org
HTTPS: https://files.wwpdb.org (replaces https://ftp.rcsb.org)
RSYNC: rsync://rsync.rcsb.org (replaces rsync://rcsb.org)

The File Download Services

documentation
has detailed information.

Starting *September 19th 2023 (1 week from now)*, RCSB PDB will start
enforcing use of these updated DNS names. URLs in which the DNS name
doesn’t match the protocol (e.g., https://ftp.rcsb.org, ftp://files.rcsb.org)
will no longer work at that time.

Users who download PDB archive data programmatically are encouraged to
switch to the new DNS names as soon as possible. HTTPS protocol is
preferred (over FTP) for individual file downloads.

Please contact i...@rcsb.org with any questions.

Many thanks

Jose

---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputer Center
UC San Diego
La Jolla CA, USA



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[ccp4bb] Postdoctoral positions - cryo-EM and biochemistry of bacterial secretion systems

[Gabriel Waksman]

Postdoctoral positions in cryo-EM and biochemistry of bacterial secretion 
systems

ISMB Birkbeck - Professor Gabriel Waksman’s laboratory

As of September 1, 2023, there is still one more position available as 
Post-doctoral Research Assistant at the ISMB to carry out structural analysis 
of the Type IV Secretion System by cryo-electron microscopy with Professor 
Gabriel Waksman. The laboratory has been exceptionally productive over the 
years in this area (see Science, 2009, 323:266-268; Nature, 2009, 
462:1011-1015; Nature, 2014, 508:550-553; Cell, 2016, 166:1436–1444; Cell, 
2017, 169:708–721; Nature. 2022, 607:191-196). The research programme is funded 
by a grant from the Medical Research Council. Further details on the research 
group and on type IV secretion can be found at:

http://people.ismb.lon.ac.uk/gabriel-waksman/homepage.htm 

Applicants should have a PhD in Structural Molecular Biology, and experience in 
Electron Microscopy, Image Processing, Biophysics, Biochemistry or related 
areas.

For instructions as to how to apply, click on the following link: 
https://cis7.bbk.ac.uk/vacancy/postdoctoral-research-assistant-537342.html 

 


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Re: [ccp4bb] Unknown density in Trypsin

[a . perrakis]

Dear Mahmoud,

The first thing to do is to make a list of (a) all your protein buffer 
components, (b) all your crystallisation conditions components, and (c) all the 
cryo-protection chemicals, and try to consider all of those as possibilities, 
but then again indeed it is most likely glycerol anyway ;-)

A,

On 12 Sep 2023, at 14:48, Maria Håkansson 
mailto:maria.hakans...@saromics.com>> wrote:

Hi Mahmoud,

It looks like glycerol (residue GOL in Coot)  to me. Add it under File/Get 
Monomer GOL.
There should be hydrogen bonds, at least one for it to turn up as well-ordered 
as below.

Good Luck!

Best regards,
Maria


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Mahmoud RIZK mailto:mahmoud.r...@esrf.fr>>
Date: Tuesday, 12 September 2023 at 14:40
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Unknown density in Trypsin
Hi everyone,
I am encountering a strong clear density within a structure of trypsin at 1.3 
Å, please find attached a 360 rotation video of it, alternatively I uploaded it 
on YouTube: https://youtube.com/shorts/tHovB55lpio?feature=share
the map shown here is a difference map at 3 sigmas.
here is the its site with respect to the protein (image below):

(PS: this blob has been detected within different trypsin structures from 
several collected data.)
(I tried 
checkmyblob.bioreproducibility.org 
without any success)

I would greatly appreciate any suggestions on how to identify and characterize 
this blob. Thank you in advance for your assistance!

With best regards,
Mahmoud




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[ccp4bb] Postdoctoral Position(s) - Mechanisms of Assemblies Formation Essential to Muscle Function

[Kristina Djinovic Carugo]

*Postdoctoral **Position**(s) - Mechanisms of Assemblies Formation 
Essential to Muscle Function*


**

EMBL Grenoble specializes in fundamental research in structural biology, 
and in developing state-of-the art instrumentation, methods and 
services. The site is located on the dynamic European Photon and Neutron 
science campus (EPN campus), together with other international and 
French research institutions.**


We are recruiting a highly motivated Post-Doctoral Scientist to join the 
Head of Unit’s Research Group at EMBL Grenoble, Kristina Djinovic 
Carugo. The Djinovic group is interested in the molecular mechanisms 
underlying the architecture and assembly of muscle sarcomeres, 
particular Z-discs.


The sarcomere - the basic contractile unit of myocytes - assembles from 
nascent actin-rich Z-bodies into paracrystalline multiprotein structures 
called Z-discs. Yet, the assembly rules and protein components 
regulating these complex structures remain largely unknown. We recently 
discovered that two main Z-disc proteins form phase-separated liquid 
condensates in vitro, which gives rise to the exciting hypothesis that 
phase separation is the driving force behind Z-disc assembly by bringing 
together its proteins to facilitate interactions.


*Djinovic Group is a member of the collaborative project “From disorder 
to order: mechanism of specialised assemblies formation essential for 
muscle function” supported by HFSP Award. Its aim is to investigate how 
highly ordered sarcomeric Z-disc structure arises from disordered 
Z-bodies. We will determine the biophysical and structural principles 
underlying sarcomere cytoskeleton assembly in biogenesis, molecular 
components, and regulators and integrate the data into a 4D multiscale 
integrative molecular model.*


The collaborative team united by HFSP Award will capitalise on 
complementary and synergistic expertise in structural biology and 
modelling (Kristina Djinovic Carugo, EMBL Grenoble; France and Toshiyuki 
Oda, University of Tokyo, Japan), advanced imaging (Jonas Ries, 
University of Vienna, Austria) and cardiovascular development and 
disease (Travis Hinson, The Jackson Laboratory, Farmington, CT, USA) and 
adopt a multifaceted and multiscale approach to tackle the central 
questions on sarcomere cytoskeleton assembly in biogenesis at the 
molecular and structural level.


*Your role*

You will embark on an exciting journey to decipher the structures of 
selected reconstituted complexes and macromolecular condensates using an 
integrative structural biology approach, which encompasses molecular 
biophysics characterisation, combined with small angles X-ray 
scattering, macromolecular crystallography, and cryo-electron 
microscopy/tomography, depending on their size and dynamics. As a team 
member, you will play a crucial role in uncovering the detailed 
biophysical and structural principles that regulate complex assembly. 
Joining collaborative efforts, you will contribute to the generation of 
a 4D multiscale integrative molecular model.


Apply now 



*Closing date:*31 October 2023

 * Contract duration: 3 years
 * Grading: stipend
 * Reference number: GR00215

*Related*

 * View all EMBL jobs 
 * Sign up for job alerts 
 * View openings from partners 

*You have*

 * PhD degree in a relevant field with strong background in structural
   biology.
 * Experience in molecular cloning, expression, and purification of
   protein complexes is essential.
 * Prior knowledge of crystallography and/or single-particle electron
   microscopy is needed.
 * Track record of writing papers as evidenced by publications or
   submitted manuscripts.
 * Ability to work independently and also to interact within a group.
 * Excellent communication skills, including the ability to write for
   publication and present results at scientific meetings.

*You might also have*

 * Previous experience in complementary structural biology methods
   (e.g. SAXS), molecular and cell biophysics approaches and cell
   culture will be considered an advantage.
 * Experience with cryo-electron tomography.
 * Experience with working in multidisciplinary research teams.

*Why join us*

EMBL is curiosity-driven, community-oriented and international. As an 
inclusive, equal opportunity employer, we believe that diversity enables 
us to collaborate more effectively and be innovative in our approaches. 
We are, therefore, committed to creating an inclusive and flexible 
culture - one where everyone can realise their full potential and make a 
positive contribution to our organisation.


We encourage applications from individuals who can complement our 
existing team – we believe that success is built on having teams whose 
backgrounds and personal experiences reflect the